Shallow eutrophic lakes commonly exist in two alternative stable states: a clear-water state and a turbid water state. A number of mechanisms, including both abiotic and biotic processes, buffer the respective states against changes, whereas other mechanisms likely drive transitions between states. Our earlier research shows that a large proportion of zooplanktivorous fish populations in shallow lakes undertake seasonal migrations where they leave the lake during winter and migrate back to the lake in spring. Based on our past research, we propose a number of scenarios of how feedback processes between the individual and ecosystem levels may affect stability of alternative stable states in shallow lakes when mediated by fish migration. Migration effects on shallow lakes result from processes at different scales, from the individual to the ecosystem. Our earlier research has shown that ecosystem properties, including piscivore abundance and zooplankton productivity, affect the individual state of zooplanktivorous fish, such as growth rate or condition. Individual state, in turn, affects the relative proportion and timing of migrating zooplanktivorous fish. This change, in turn, may stabilize states or cause runaway processes that eventually lead to state shifts. Consequently, such knowledge of processes coupled to seasonal migration of planktivorous fish should increase our understanding of shallow lake dynamics.